The problem hasn't been solved
Hello all - brand new to using pyrosetta so apologies if I'm missing something obvious.
Hi all! I am attempting my very first enzyme design campaign and running into issues with matching. I generated a cstfile from averaging native pdb measurements within a family, and am trying to match my theozyme (a new substrate - LFF) to one representative structure as a test (PDB ID: 5nci chain A).
When I run:
Dear all,
I generated a silent file as a result of a docking refinement with FlexPepDock. I want to anaylize the top 10% of the solutions (1000 decoys) and cluster them.
First, I extracted the top 10% by sorting the I_sc with:
sort -n -k2 example_score_file.sc | head -n 1000 | awk '{print $2 "\t" $25 "\t" $NF}' > score_I-sc_tag.dat
Hi, looking for some help,
It appears that constraints do not contribute to the final score output when running the FlexPepDock ab initio protocol.
I am getting docking samples that should yield score penalties >1000 under the provided distance constraints (AtomPair FLAT_HARMONIC). However, the scorefile reports numbers consistent with the score absent of penalties (approx -550, for a protein length 300 and peptide length 5).
I provide the constraints file with the flag -constraints:cst_file
Hi there,
I've noticed that the FlexPepDock ab initio protocol will run even if fragments aren't specified. It also appears during these runs that the peptide backbone is flexible, varying between samples.
When no fragments are specified, what does the FlexPepDock application do to ab initio model peptides exactly?
Is there a 'default' set of fragments?
Thank you!
Nathan
Hi,
I just downloaded the 3.13 tarball (precompiled binaries) and when I extracted it, the directory structure says it's rosetta_bin_linux_2021.16.61629_bundle (the previous version). Additionally, the md5sum values for all of the tarballs also point to 2021.16.61629. Can you upload the 3.13 version?
Best,
Ken
Currently to get the number of iterations a mover, such as FastRelax does, I enable the dump_trajectory scoretype and count the models in the PDBs (code below).
This seems very very weird way of doing this, so I was wondering if there is a less silly way of doing this?
Also, is there a direct way to open a multimodel file say to get the scores of each? (Rather than extracting the models, writing to file, reading them into PyRosetta and scoring them).
The compiled downloads of pyrosetta from Rosetta commons* aren't '--serialization' builds.
* I was going to doublecheck but https://www.rosettacommons.org/software/license-and-download is giving me a 404 for PyRosetta.
Is there any disadavantage in this build one should be wary of? Like slower, segfault-y-er, lacking other features etc.
The fact that it is not one of the options makes me think there may be, hence my asking.
